Merge branch 'master' into core-updates.

Conflicts:
	gnu/local.mk
	gnu/packages/build-tools.scm
	gnu/packages/certs.scm
	gnu/packages/check.scm
	gnu/packages/compression.scm
	gnu/packages/cups.scm
	gnu/packages/fontutils.scm
	gnu/packages/gnuzilla.scm
	gnu/packages/guile.scm
	gnu/packages/ibus.scm
	gnu/packages/image-processing.scm
	gnu/packages/linux.scm
	gnu/packages/music.scm
	gnu/packages/nss.scm
	gnu/packages/pdf.scm
	gnu/packages/python-xyz.scm
	gnu/packages/qt.scm
	gnu/packages/ruby.scm
	gnu/packages/shells.scm
	gnu/packages/tex.scm
	gnu/packages/video.scm
	gnu/packages/vulkan.scm
	gnu/packages/web.scm
	gnu/packages/webkit.scm
	gnu/packages/wm.scm

1 files changed, 133 insertions, 2 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f157523a76..cb12eba7c5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3521,8 +3521,6 @@ annotations of the genome.")
     ;; remainder of the code is licensed under the MIT license.
     (license (list license:bsd-3 license:expat))))
 
-(define-deprecated deeptools python-deeptools)
-
 (define-public cutadapt
   (package
     (name "cutadapt")
@@ -13991,6 +13989,85 @@ cells with similar identification cards in the different cytometric profiles
 is then merged.")
       (license license:gpl2))))
 
+(define-public r-cytoexplorer
+  (let ((commit "0efb1cc19fc701ae03905cf1b8484c1dfeb387df")
+        (revision "1"))
+    (package
+      (name "r-cytoexplorer")
+      (version (git-version "1.1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/DillonHammill/CytoExploreR")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1y7dadsy15i47rjmdq6ns80jzm6p0zmixll37q68ba2c7xn5pq3v"))
+         (snippet
+          '(delete-file
+            "docs/articles/CytoExploreR_files/vis-4.20.1/vis.min.js"))))
+      (properties `((upstream-name . "CytoExploreR")))
+      (build-system r-build-system)
+      (arguments
+       (list
+        #:phases
+        '(modify-phases %standard-phases
+           (add-after 'unpack 'process-javascript
+             (lambda* (#:key inputs #:allow-other-keys)
+               (with-directory-excursion "docs/articles/CytoExploreR_files/"
+                 (let ((source (search-input-file inputs "/dist/vis.js"))
+                       (target "vis-4.20.1/vis.min.js"))
+                   (invoke "esbuild" source "--minify"
+                           (string-append "--outfile=" target)))))))))
+      (propagated-inputs
+       (list r-biocgenerics
+             r-bslib
+             r-data-table
+             r-dplyr
+             r-embedsom
+             r-flowai
+             r-flowcore
+             r-flowworkspace
+             r-gtools
+             r-magrittr
+             r-mass
+             r-opencyto
+             r-purrr
+             r-rhandsontable
+             r-robustbase
+             r-rsvd
+             r-rtsne
+             r-shiny
+             r-superheat
+             r-tibble
+             r-tidyr
+             r-umap
+             r-visnetwork))
+      (native-inputs
+       `(("esbuild" ,esbuild)
+         ("r-knitr" ,r-knitr)
+         ("js-vis"
+          ,(let ((version "4.20.1"))
+             (origin
+               (method git-fetch)
+               (uri (git-reference
+                     (url "https://github.com/almende/vis")
+                     (commit (string-append "v" version))))
+               (file-name (git-file-name "js-vis" version))
+               (sha256
+                (base32
+                 "09ldcqzzki5c0jlwas5992qjffqxnx6j5sl703qccfw7rg1hn469")))))))
+      (home-page "https://github.com/DillonHammill/CytoExploreR")
+      (synopsis "Interactive analysis of cytometry data")
+      (description
+       "This package has been developed under ROpenSci gudelines to integrate
+conventional and cutting edge cytometry analysis tools under a unified
+framework.  It aims to represent an intuitive and interactive approach to
+analysing cytometry data in R.")
+      (license license:gpl2))))
+
 (define-public r-giotto
   (let ((commit "3c8067cedbf6e3112edcac2ae796de05fd9d6fe4")
         (revision "1"))
@@ -14049,6 +14126,60 @@ is then merged.")
 spatial single-cell expression data.")
       (license license:expat))))
 
+(define-public r-illuminahumanmethylationepicanno-ilm10b5-hg38
+  (let ((commit "3db06910e27f626e0cc8b335ff45cf9a4050a36a")
+        (revision "1"))
+    (package
+      (name "r-illuminahumanmethylationepicanno-ilm10b5-hg38")
+      (version (git-version "0.0.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url
+                       "https://github.com/achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0y8fhiwmkldi57f8nq64njfgljw68cm6pb1vh44hjwcc12k48sqr"))))
+      (properties `((upstream-name . "IlluminaHumanMethylationEPICanno.ilm10b5.hg38")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-minfi))
+      (home-page
+       "https://github.com/achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38")
+      (synopsis "Illumina Human Methylation EPIC Annotation version 1.0B5")
+      (description
+       "This package provides a companion annotation file to the
+@code{IlluminaHumanMethylationEPICmanifest} package based on the same
+annotation 1.0B5.")
+      (license license:artistic2.0))))
+
+(define-public r-maxprobes
+  (let ((commit "c2120dba972e12115280ef274ff80550cee5b264")
+        (revision "1"))
+    (package
+      (name "r-maxprobes")
+      (version (git-version "0.0.2" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/markgene/maxprobes")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1kij9bds2l9mwm519bzyd2608563qjlmbrayhva1s0vgml5iq9wh"))))
+      (properties `((upstream-name . "maxprobes")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-minfi r-minfidata))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/markgene/maxprobes")
+      (synopsis "Methylation array cross-reactive probes")
+      (description
+       "The Maxprobes package collects cross-reactive probes of Illumina
+methylation array 450K and EPIC/850K.")
+      (license license:gpl2+))))
+
 (define-public gffread
   ;; We cannot use the tagged release because it is not in sync with gclib.
   ;; See https://github.com/gpertea/gffread/issues/26